SMTL ID : 2qv6.1

GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: D.230 Chain C: R.22, E.24, L.27 Ligands: GTP.4 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:R.22, C:E.24, A:D.230, H2O.5 K.5: 4 residues within 4Å: Chain B: D.230 Chain D: R.22, E.24 Ligands: GTP.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Metal complexes: B:D.230, D:R.22, D:E.24 K.9: 5 residues within 4Å: Chain A: R.22, E.24, L.27 Chain C: D.230 Ligands: GTP.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:R.22, A:E.24, C:D.230 K.13: 4 residues within 4Å: Chain B: R.22, E.24 Chain D: D.230 Ligands: GTP.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Metal complexes: B:R.22, B:E.24, D:D.230

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.138, I.139, D.183, K.213 Ligands: NA.3, GTP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.138, A:D.138, A:I.139, A:D.183 CA.6: 5 residues within 4Å: Chain B: D.138, I.139, D.183 Ligands: NA.7, GTP.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.138, B:D.138, B:I.139, B:D.183 CA.10: 5 residues within 4Å: Chain C: D.138, I.139, D.183 Ligands: NA.11, GTP.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.138, C:D.138, C:I.139, C:D.183 CA.14: 7 residues within 4Å: Chain D: D.138, I.139, D.183, K.213, R.237 Ligands: NA.15, GTP.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.138, D:D.138, D:I.139, D:D.183

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: D.138, D.183, N.184 Ligands: CA.2, GTP.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.183, A:N.184 NA.7: 5 residues within 4Å: Chain B: D.138, D.183, N.184 Ligands: CA.6, GTP.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.138, B:N.184 NA.11: 5 residues within 4Å: Chain C: D.138, D.183, N.184 Ligands: CA.10, GTP.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.183, C:N.184 NA.15: 5 residues within 4Å: Chain D: D.138, D.183, N.184 Ligands: CA.14, GTP.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.183, D:N.184

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.4: 25 residues within 4Å: Chain A: H.136, D.138, I.139, N.140, N.141, I.142, T.143, I.180, G.181, G.182, D.183, N.184, K.213, R.237 Chain C: Y.12, G.13, T.16, E.24, L.27, Q.28, D.55, Q.112 Ligands: K.1, CA.2, NA.3 19 PLIP interactions: 11 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:D.138, A:N.141, A:I.142, A:T.143, A:T.143, A:I.180, A:N.184, C:G.13, C:D.55, C:Q.112 Water bridges: A:R.237, C:Y.12, C:Q.31, C:Q.31, C:D.55 Salt bridges: A:K.213, A:R.237, A:R.237, C:E.24 GTP.8: 25 residues within 4Å: Chain B: H.136, D.138, I.139, N.140, N.141, I.142, T.143, I.180, G.181, G.182, D.183, N.184, K.213, R.237 Chain D: Y.12, G.13, T.16, E.24, L.27, Q.28, D.55, Q.112 Ligands: K.5, CA.6, NA.7 21 PLIP interactions: 10 interactions with chain D, 11 interactions with chain B Hydrogen bonds: D:G.13, D:T.16, D:Q.28, D:D.55, D:D.55, D:Q.112, B:D.138, B:N.141, B:I.142, B:T.143, B:I.180, B:N.184 Water bridges: D:Q.31, D:Q.31, D:D.55, B:R.237, B:R.237 Salt bridges: D:E.24, B:K.213, B:R.237, B:R.237 GTP.12: 25 residues within 4Å: Chain A: Y.12, G.13, T.16, E.24, L.27, Q.28, D.55, Q.112 Chain C: H.136, D.138, I.139, N.140, N.141, I.142, T.143, I.180, G.181, G.182, D.183, N.184, K.213, R.237 Ligands: K.9, CA.10, NA.11 23 PLIP interactions: 14 interactions with chain C, 9 interactions with chain A Hydrogen bonds: C:D.138, C:N.141, C:N.141, C:I.142, C:T.143, C:T.143, C:I.180, C:D.183, C:N.184, A:T.16, A:D.55, A:D.55, A:Q.112 Water bridges: C:R.237, C:R.237, A:Y.12, A:Q.31, A:Q.31, A:D.55 Salt bridges: C:K.213, C:R.237, C:R.237, A:E.24 GTP.16: 25 residues within 4Å: Chain B: Y.12, G.13, T.16, E.24, L.27, Q.28, D.55, Q.112 Chain D: H.136, D.138, I.139, N.140, N.141, I.142, T.143, I.180, G.181, G.182, D.183, N.184, K.213, R.237 Ligands: K.13, CA.14, NA.15 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain D Hydrogen bonds: B:Q.28, B:D.55, B:Q.112, D:D.138, D:N.141, D:I.142, D:T.143, D:I.180, D:N.184 Water bridges: B:Y.12, B:G.13, B:Q.31, B:Q.31, B:D.55, D:R.237 Salt bridges: B:E.24, D:K.213, D:R.237, D:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morrison, S.D. et al., A New Use for a Familiar Fold: The X-ray Crystal Structure of GTP-Bound GTP Cyclohydrolase III from Methanocaldococcus jannaschii Reveals a Two Metal Ion Catalytic Mechanism. Biochemistry (2008)

Release Date

2008-01-15

Peptides

GTP cyclohydrolase III: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GTP cyclohydrolase III